Author

R. Mehra

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Open access Jul 2026

Solvent-buffer effects in molecular dynamics simulations of nucleic acids

The results show that while the commonly used 10 Å buffer may be sufficient to maintain the stability of the double-stranded nucleic acid, larger cells are required to capture the conformational dynamics of single-stranded structures.

Nainsy Baghel, Pranchal Shrivastava, R. Mehra · bioRxiv · 0 citations

Open access Aug 2026

DeepPNI: a language- and graph-based model for mutation-driven protein–nucleic acid binding energetics

DeepPNI is a deep learning regression model that integrates sequence- and structure-based features to estimate mutation-induced changes in binding free energy in protein–nucleic acid complexes, developed using a comprehensive dataset of 1754 mutations spanning protein–DNA and protein–RNA complexes.

Somnath Mondal, Tinkal Mondal, Soumajit Pramanik et al. · Nucleic Acids Research · 0 citations